Gst_prime: Estimation Nei's Gst parameter with Hedrick's correction for...
In dyerlab/gstudio: Tools Related to the Spatial Analysis of Genetic Marker Data

Gst_prime

R Documentation

Estimation Nei's Gst parameter with Hedrick's correction for allelic diversity

Description

This function estimates the parameter (and potentially the confidence surrounding its value) for Gst. It is corrected by the diversity of the parameter as outlined by Hedrick.

Usage

Gst_prime(x, stratum = "Population", nperm = 0, size.correct = TRUE)

Arguments

`x`	A vector of `locus` objects or a `data.frame` with `locus` objects.
`stratum`	Either a vector of strata variables if `x` is a `locus` vector or the name of the column representing strata in `x` if it is a `data.frame`.
`nperm`	The number of permutations to run for significance of the estimator.
`size.correct`	A flag indicating that the estimate should be corrected for based upon sample sizes (default=TRUE).

Value

An data.frame with Gst, Ht, and Hs and optionally P. If more than one locus is provided, then a 'mutlilocus' estimate is shown using the harmonic mean of individual locus Gst_prime values.

Author(s)

Rodney J. Dyer rjdyer@vcu.edu

Examples

 a1 <- sample( LETTERS[1:5], size=20, replace=TRUE)
 a2 <- sample( LETTERS[4:8], size=20, replace=TRUE)
 raw_alleles <- matrix( c(a1,a2), ncol=2, byrow=TRUE )
 locus <- locus( raw_alleles, type="column")
 Population <- c(rep("Pop-A",10),rep("Pop-B",10))
 Gst_prime( locus, Population )
 a1 <- sample( LETTERS[1:5], size=20, replace=TRUE)
 a2 <- sample( LETTERS[4:8], size=20, replace=TRUE)
 raw_alleles <- matrix( c(a1,a2), ncol=2, byrow=TRUE )
 locus2 <- locus( raw_alleles, type="column")
 df <- data.frame( Population, TPI=locus, PGM=locus2 )
 Gst_prime( df, nperm=99)

dyerlab/gstudio documentation built on Feb. 2, 2024, 8:24 p.m.